Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China.
PLoS One. 2013 Apr 22;8(4):e62308. doi: 10.1371/journal.pone.0062308. Print 2013.
The crucian carp is an important aquaculture species and a potential model to study genome evolution and physiological adaptation. However, so far the genomics and transcriptomics data available for this species are still scarce. We performed de novo transcriptome sequencing of four cDNA libraries representing brain, muscle, liver and kidney tissues respectively, each with six specimens. The removal of low quality reads resulted in 2.62 million raw reads, which were assembled as 127,711 unigenes, including 84,867 isotigs and 42,844 singletons. A total of 22,273 unigenes were found with significant matches to 14,449 unique proteins. Around14,398 unigenes were assigned with at least one Gene Ontology (GO) category in 84,876 total assignments, and 6,382 unigenes were found in 237 predicted KEGG pathways. The gene expression analysis revealed more genes expressed in brain, more up-regulated genes in muscle and more down-regulated genes in liver as compared with gene expression profiles of other tissues. In addition, 23 enzymes in the glycolysis/gluconeogenesis pathway were recovered. Importantly, we identified 5,784 high-quality putative SNP and 11,295 microsatellite markers which include 5,364 microsatellites with flanking sequences ≥50 bp. This study produced the most comprehensive genomic resources that have been derived from crucian carp, including thousands of genetic markers, which will not only lay a foundation for further studies on polyploidy origin and anoxic survival but will also facilitate selective breeding of this important aquaculture species.
鲫鱼是一种重要的水产养殖物种，也是研究基因组进化和生理适应的潜在模式生物。然而，迄今为止，该物种的基因组学和转录组学数据仍然很少。我们分别对代表脑、肌肉、肝脏和肾脏组织的四个 cDNA 文库进行了从头转录组测序，每个文库有 6 个样本。去除低质量的读取后，得到了 262 万条原始读取，这些读取被组装成 127711 个非重叠基因，其中包括 84867 个 iso-tigs 和 42844 个 singletons。共有 22273 个基因与 14449 个独特蛋白质有显著匹配。在 84876 个总分配中，约有 14398 个基因被分配到至少一个基因本体论（GO）类别，在 237 个预测的 KEGG 途径中发现了 6382 个基因。基因表达分析显示，与其他组织的基因表达谱相比，大脑中的基因表达更多，肌肉中的上调基因更多，肝脏中的下调基因更多。此外，还恢复了糖酵解/糖异生途径中的 23 种酶。重要的是，我们鉴定了 5784 个高质量的候选 SNP 和 11295 个微卫星标记，其中包括 5364 个侧翼序列≥50bp 的微卫星。这项研究提供了最全面的鲫鱼基因组资源，包括数千个遗传标记，这不仅为进一步研究多倍体起源和缺氧生存奠定了基础，也为这一重要水产养殖物种的选育提供了便利。
